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Merge branch 'Development' of https://gitlab.eudat.eu/dmp/OpenAIRE-EUDAT-DMP-service-pilot into Development

This commit is contained in:
Diamantis Tziotzios 2021-07-07 20:40:24 +03:00
parent b8b78f6653 6e21ad127d
commit ad245dde5d
40 changed files with 784 additions and 178 deletions
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8
dmp-backend/data/src/main/java/eu/eudat/data/entities/DMP.java
View File

@ -15,11 +15,11 @@ import java.util.stream.Collectors;
@NamedEntityGraphs({
@NamedEntityGraph(
name = "dataManagementPlanListingModel",
attributeNodes = {@NamedAttributeNode("organisations"), @NamedAttributeNode("researchers"), @NamedAttributeNode("associatedDmps"),
@NamedAttributeNode("grant"), @NamedAttributeNode(value = "users", subgraph = "users"), @NamedAttributeNode("creator"), @NamedAttributeNode("profile"), @NamedAttributeNode("dataset")},
subgraphs = {
attributeNodes = {
@NamedAttributeNode("grant"), @NamedAttributeNode("creator"), @NamedAttributeNode("profile")}/*,*/
/*subgraphs = {
@NamedSubgraph(name = "users", attributeNodes = {@NamedAttributeNode("user")}),
}
}*/
),
@NamedEntityGraph(
name = "fullyDetailed",

4
dmp-backend/data/src/main/java/eu/eudat/data/query/definition/helpers/ColumnOrderings.java
View File

@ -34,6 +34,10 @@ public class ColumnOrderings {
ordering.fieldName(ordering.getFieldName().replace("|count|", "")).columnType(Ordering.ColumnType.COUNT);
else if (ordering.getFieldName().contains("|join|"))
ordering.fieldName(ordering.getFieldName().replace("|join|", "")).columnType(Ordering.ColumnType.JOIN_COLUMN);
else if (ordering.getFieldName().equals("asc"))
ordering.fieldName("label").orderByType(Ordering.OrderByType.ASC);
else if (ordering.getFieldName().equals("desc"))
ordering.fieldName("label").orderByType(Ordering.OrderByType.DESC);
return ordering;
}
}

27
dmp-backend/elastic/src/main/java/eu/eudat/elastic/criteria/DatasetCriteria.java
View File

@ -21,6 +21,9 @@ public class DatasetCriteria extends Criteria {
private List<Tag> tags;
private boolean isPublic;
private Short grantStatus;
private int offset;
private int size;
private List<SortCriteria> sortCriteria;
public String getLike() {
return like;
@ -117,4 +120,28 @@ public class DatasetCriteria extends Criteria {
public void setGrantStatus(Short grantStatus) {
this.grantStatus = grantStatus;
}
public int getOffset() {
return offset;
}
public void setOffset(int offset) {
this.offset = offset;
}
public int getSize() {
return size;
}
public void setSize(int size) {
this.size = size;
}
public List<SortCriteria> getSortCriteria() {
return sortCriteria;
}
public void setSortCriteria(List<SortCriteria> sortCriteria) {
this.sortCriteria = sortCriteria;
}
}

37
dmp-backend/elastic/src/main/java/eu/eudat/elastic/criteria/DmpCriteria.java
View File

@ -9,11 +9,16 @@ public class DmpCriteria extends Criteria {
private List<UUID> templates;
private List<UUID> grants;
private List<UUID> collaborators;
private List<Integer> roles;
private List<UUID> organizations;
private boolean isPublic;
private List<UUID> groupIds;
private boolean allowAllVersions;
private Short grantStatus;
private int offset;
private Integer size;
private List<SortCriteria> sortCriteria;
public String getLike() {
return like;
@ -55,6 +60,14 @@ public class DmpCriteria extends Criteria {
this.collaborators = collaborators;
}
public List<Integer> getRoles() {
return roles;
}
public void setRoles(List<Integer> roles) {
this.roles = roles;
}
public List<UUID> getOrganizations() {
return organizations;
}
@ -94,4 +107,28 @@ public class DmpCriteria extends Criteria {
public void setGrantStatus(Short grantStatus) {
this.grantStatus = grantStatus;
}
public int getOffset() {
return offset;
}
public void setOffset(int offset) {
this.offset = offset;
}
public Integer getSize() {
return size;
}
public void setSize(Integer size) {
this.size = size;
}
public List<SortCriteria> getSortCriteria() {
return sortCriteria;
}
public void setSortCriteria(List<SortCriteria> sortCriteria) {
this.sortCriteria = sortCriteria;
}
}

39
dmp-backend/elastic/src/main/java/eu/eudat/elastic/criteria/SortCriteria.java Normal file
View File

@ -0,0 +1,39 @@
package eu.eudat.elastic.criteria;
public class SortCriteria {
public enum OrderByType {
ASC, DESC
}
public enum ColumnType {
COUNT, COLUMN, JOIN_COLUMN
}
private String fieldName;
private OrderByType orderByType;
private ColumnType columnType;
public String getFieldName() {
return fieldName;
}
public void setFieldName(String fieldName) {
this.fieldName = fieldName;
}
public OrderByType getOrderByType() {
return orderByType;
}
public void setOrderByType(OrderByType orderByType) {
this.orderByType = orderByType;
}
public ColumnType getColumnType() {
return columnType;
}
public void setColumnType(ColumnType columnType) {
this.columnType = columnType;
}
}

12
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Collaborator.java
View File

@ -4,11 +4,11 @@ import org.elasticsearch.common.xcontent.XContentBuilder;
import java.io.IOException;
import java.util.Map;
import java.util.UUID;
public class Collaborator implements ElasticEntity<Collaborator> {
private String id;
private String name;
private int role;
public String getId() {
return id;
@ -26,11 +26,20 @@ public class Collaborator implements ElasticEntity<Collaborator> {
this.name = name;
}
public int getRole() {
return role;
}
public void setRole(int role) {
this.role = role;
}
@Override
public XContentBuilder toElasticEntity(XContentBuilder builder) throws IOException {
builder.startObject();
builder.field("id", this.id);
builder.field("name", this.name);
builder.field("role", this.role);
builder.endObject();
return builder;
}
@ -39,6 +48,7 @@ public class Collaborator implements ElasticEntity<Collaborator> {
public Collaborator fromElasticEntity(Map fields) {
this.id = (String) fields.get("id");
this.name = (String) fields.get("name");
this.role = (int) fields.get("role");
return this;
}
}

37
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Dataset.java
View File

@ -5,6 +5,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.time.Instant;
import java.util.*;
import java.util.stream.Collectors;
@ -59,6 +60,9 @@ public class Dataset implements ElasticEntity<Dataset> {
private Boolean isPublic;
private Short grantStatus;
private String formData;
private Date created;
private Date modified;
private Date finalizedAt;
public String getId() {
return id;
@ -188,6 +192,30 @@ public class Dataset implements ElasticEntity<Dataset> {
this.formData = formData;
}
public Date getCreated() {
return created;
}
public void setCreated(Date created) {
this.created = created;
}
public Date getModified() {
return modified;
}
public void setModified(Date modified) {
this.modified = modified;
}
public Date getFinalizedAt() {
return finalizedAt;
}
public void setFinalizedAt(Date finalizedAt) {
this.finalizedAt = finalizedAt;
}
@Override
public XContentBuilder toElasticEntity(XContentBuilder builder) throws IOException {
builder.startObject();
@ -197,6 +225,9 @@ public class Dataset implements ElasticEntity<Dataset> {
builder.field("template", this.template.toString());
builder.field("status", this.status.toString());
builder.field("dmp", this.dmp.toString());
builder.field("created", this.created);
builder.field("modified", this.modified);
builder.field("finalizedAt", this.finalizedAt);
if (this.group != null) {
builder.field("group", this.group.toString());
}
@ -263,6 +294,12 @@ public class Dataset implements ElasticEntity<Dataset> {
this.dmp = UUID.fromString((String) fields.get("dmp"));
this.group = UUID.fromString((String) fields.get("group"));
this.grant = UUID.fromString((String) fields.get("grant"));
if (fields.get("created") != null)
this.created = Date.from(Instant.parse((String) fields.get("created")));
if (fields.get("modified") != null)
this.modified = Date.from(Instant.parse((String) fields.get("modified")));
if (fields.get("finalizedAt") != null)
this.finalizedAt = Date.from(Instant.parse((String) fields.get("finalizedAt")));
if (fields.get("collaborators") != null) {
this.collaborators = ((List<HashMap>) fields.get("collaborators")).stream().map(hashMap -> new Collaborator().fromElasticEntity(hashMap)).collect(Collectors.toList());
}

62
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Dmp.java
View File

@ -5,10 +5,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import java.util.*;
import java.util.stream.Collectors;
public class Dmp implements ElasticEntity<Dmp> {
@ -55,6 +52,11 @@ public class Dmp implements ElasticEntity<Dmp> {
private List<Dataset> datasets;
private UUID grant;
private Short grantStatus;
private Date created;
private Date modified;
private Date finalizedAt;
private Date publishedAt;
private String doi;
public UUID getId() {
return id;
@ -168,6 +170,46 @@ public class Dmp implements ElasticEntity<Dmp> {
this.grantStatus = grantStatus;
}
public Date getCreated() {
return created;
}
public void setCreated(Date created) {
this.created = created;
}
public Date getModified() {
return modified;
}
public void setModified(Date modified) {
this.modified = modified;
}
public Date getFinalizedAt() {
return finalizedAt;
}
public void setFinalizedAt(Date finalizedAt) {
this.finalizedAt = finalizedAt;
}
public Date getPublishedAt() {
return publishedAt;
}
public void setPublishedAt(Date publishedAt) {
this.publishedAt = publishedAt;
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
@Override
public XContentBuilder toElasticEntity(XContentBuilder builder) throws IOException {
builder.startObject();
@ -233,6 +275,11 @@ public class Dmp implements ElasticEntity<Dmp> {
builder.field(MapKey.GRANT.getName(), this.grant.toString());
}
builder.field(MapKey.GRANTSTATUS.getName(), this.grantStatus);
builder.field(MapKey.CREATED.getName(), this.created);
builder.field(MapKey.MODIFIED.getName(), this.modified);
builder.field(MapKey.FINALIZEDAT.getName(), this.finalizedAt);
builder.field(MapKey.PUBLISHEDAT.getName(), this.publishedAt);
builder.field(MapKey.DOI.getName(), this.doi);
builder.endObject();
return builder;
}
@ -282,7 +329,12 @@ public class Dmp implements ElasticEntity<Dmp> {
ISPUBLIC ("isPublic"),
DATASETS ("datasets"),
GRANT ("grant"),
GRANTSTATUS ("grantStatus");
GRANTSTATUS ("grantStatus"),
CREATED ("created"),
MODIFIED ("modified"),
FINALIZEDAT ("finalizedAt"),
PUBLISHEDAT ("publishedAt"),
DOI ("doi");
private final String name;

24
dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/DatasetRepository.java
View File

@ -24,6 +24,9 @@ import org.elasticsearch.search.aggregations.bucket.filter.ParsedFilters;
import org.elasticsearch.search.aggregations.bucket.nested.NestedAggregationBuilder;
import org.elasticsearch.search.aggregations.bucket.nested.ParsedNested;
import org.elasticsearch.search.builder.SearchSourceBuilder;
import org.elasticsearch.search.sort.SortBuilder;
import org.elasticsearch.search.sort.SortBuilders;
import org.elasticsearch.search.sort.SortOrder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.env.Environment;
@ -120,6 +123,7 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
searchSourceBuilder.size(count.intValue());
BoolQueryBuilder boolQuery = QueryBuilders.boolQuery().mustNot(QueryBuilders.termsQuery("datasets.status", Stream.of(Dataset.Status.DELETED.getValue(), Dataset.Status.CANCELED.getValue()).collect(Collectors.toList())));
List<SortBuilder> sortBuilders = new ArrayList<>();
if (criteria.isPublic()) {
boolQuery = boolQuery.should(QueryBuilders.termQuery("datasets.public", "true"));
boolQuery = boolQuery.should(QueryBuilders.termQuery("datasets.status", Dataset.Status.FINALISED.getValue()));
@ -181,8 +185,26 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
boolQuery.minimumShouldMatch(boolQuery.should().size());
}
if (criteria.getSortCriteria() != null && !criteria.getSortCriteria().isEmpty()) {
criteria.getSortCriteria().forEach(sortCriteria -> {
switch(sortCriteria.getColumnType()) {
case COLUMN:
sortBuilders.add(SortBuilders.fieldSort(sortCriteria.getFieldName()).order(SortOrder.fromString(sortCriteria.getOrderByType().name())));
break;
case JOIN_COLUMN:
List<String> fields = Arrays.asList(sortCriteria.getFieldName().split(":"));
fields.stream().filter(name -> !name.startsWith("dmp")).forEach(field -> {
sortBuilders.add(SortBuilders.fieldSort(field).order(SortOrder.fromString(sortCriteria.getOrderByType().name())));
});
break;
}
});
}
NestedQueryBuilder nestedQueryBuilder = QueryBuilders.nestedQuery("datasets", boolQuery, ScoreMode.Avg).innerHit(new InnerHitBuilder());
searchSourceBuilder.query(nestedQueryBuilder);
searchSourceBuilder.query(nestedQueryBuilder).from(criteria.getOffset()).size(criteria.getSize());
sortBuilders.forEach(searchSourceBuilder::sort);
searchRequest.source(searchSourceBuilder);
SearchResponse response = this.getClient().search(searchRequest, RequestOptions.DEFAULT);
return ((Stream<Dataset>)Arrays.stream(response.getHits().getHits())

94
dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/DmpRepository.java
View File

@ -23,6 +23,9 @@ import org.elasticsearch.index.query.BoolQueryBuilder;
import org.elasticsearch.index.query.QueryBuilders;
import org.elasticsearch.index.reindex.DeleteByQueryRequest;
import org.elasticsearch.search.builder.SearchSourceBuilder;
import org.elasticsearch.search.sort.SortBuilder;
import org.elasticsearch.search.sort.SortBuilders;
import org.elasticsearch.search.sort.SortOrder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -97,6 +100,7 @@ public class DmpRepository extends ElasticRepository<Dmp, DmpCriteria> {
searchSourceBuilder.size(count.intValue());
BoolQueryBuilder boolQuery = QueryBuilders.boolQuery().mustNot(QueryBuilders.termsQuery(Dmp.MapKey.STATUS.getName(), Collections.singletonList(Dmp.DMPStatus.DELETED.getValue())));
List<SortBuilder> sortBuilders = new ArrayList<>();
if (criteria.isPublic()) {
boolQuery = boolQuery.should(QueryBuilders.termQuery(Dmp.MapKey.ISPUBLIC.getName(), true));
boolQuery = boolQuery.should(QueryBuilders.termQuery(Dmp.MapKey.STATUS.getName(), Dmp.DMPStatus.FINALISED.getValue()));
@ -125,7 +129,11 @@ public class DmpRepository extends ElasticRepository<Dmp, DmpCriteria> {
}
if (criteria.getCollaborators() != null && criteria.getCollaborators().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.COLLABORATORS.getName() + ".keyword", criteria.getCollaborators().stream().map(UUID::toString).collect(Collectors.toList())));
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.COLLABORATORS.getName() + ".id.keyword", criteria.getCollaborators().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getRoles() != null && criteria.getRoles().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.COLLABORATORS.getName() + ".role.keyword", criteria.getRoles()));
}
if (!criteria.isAllowAllVersions()) {
@ -145,7 +153,28 @@ public class DmpRepository extends ElasticRepository<Dmp, DmpCriteria> {
} else {
boolQuery.minimumShouldMatch(boolQuery.should().size());
}
searchSourceBuilder.query(boolQuery);
if (criteria.getSortCriteria() != null && !criteria.getSortCriteria().isEmpty()) {
criteria.getSortCriteria().forEach(sortCriteria -> {
switch(sortCriteria.getColumnType()) {
case COLUMN:
sortBuilders.add(SortBuilders.fieldSort(sortCriteria.getFieldName()).order(SortOrder.fromString(sortCriteria.getOrderByType().name())));
break;
case JOIN_COLUMN:
List<String> fields = Arrays.asList(sortCriteria.getFieldName().split(":"));
fields.forEach(field -> {
sortBuilders.add(SortBuilders.fieldSort(sortCriteria.getFieldName()).order(SortOrder.fromString(sortCriteria.getOrderByType().name())));
});
break;
}
});
}
searchSourceBuilder.query(boolQuery).from(criteria.getOffset());
if (criteria.getSize() != null) {
searchSourceBuilder.size(criteria.getSize());
}
sortBuilders.forEach(searchSourceBuilder::sort);
searchRequest.source(searchSourceBuilder);
SearchResponse response = this.getClient().search(searchRequest, RequestOptions.DEFAULT);
return Arrays.stream(response.getHits().getHits()).map(x -> new Dmp().fromElasticEntity((Map<String, Object>) this.transformFromString(x.getSourceAsString(), Map.class))).collect(Collectors.toList());
@ -153,6 +182,67 @@ public class DmpRepository extends ElasticRepository<Dmp, DmpCriteria> {
return null;
}
public Long count(DmpCriteria criteria) throws IOException {
if (this.getClient() != null) {
CountRequest countRequest = new CountRequest(this.environment.getProperty("elasticsearch.index"));
BoolQueryBuilder boolQuery = QueryBuilders.boolQuery().mustNot(QueryBuilders.termsQuery(Dmp.MapKey.STATUS.getName(), Collections.singletonList(Dmp.DMPStatus.DELETED.getValue())));
if (criteria.isPublic()) {
boolQuery = boolQuery.should(QueryBuilders.termQuery(Dmp.MapKey.ISPUBLIC.getName(), true));
boolQuery = boolQuery.should(QueryBuilders.termQuery(Dmp.MapKey.STATUS.getName(), Dmp.DMPStatus.FINALISED.getValue()));
}
if (criteria.getLike() != null && !criteria.getLike().isEmpty()) {
boolQuery = boolQuery.should(QueryBuilders.queryStringQuery(criteria.getLike()).fields(Stream.of(new Object[][]{
{Dmp.MapKey.LABEL.getName(), 1.0f},
{Dmp.MapKey.DESCRIPTION.getName(), 1.0f}
}).collect(Collectors.toMap(data -> (String) data[0], data -> (Float) data[1]))));
}
if (criteria.getTemplates() != null && criteria.getTemplates().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.TEMPLATES.getName() + ".id.keyword", criteria.getTemplates().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getStatus() != null) {
boolQuery = boolQuery.should(QueryBuilders.termQuery(Dmp.MapKey.STATUS.getName(), criteria.getStatus().intValue()));
}
if (criteria.getGroupIds() != null && criteria.getGroupIds().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.GROUPID.getName(), criteria.getGroupIds().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getGrants() != null && criteria.getGrants().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.GRANT.getName() + ".keyword", criteria.getGrants().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getCollaborators() != null && criteria.getCollaborators().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.COLLABORATORS.getName() + ".id.keyword", criteria.getCollaborators().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (!criteria.isAllowAllVersions()) {
boolQuery = boolQuery.should(QueryBuilders.termQuery(criteria.isPublic() ? Dmp.MapKey.LASTPUBLICVERSION.getName() : Dmp.MapKey.LASTVERSION.getName(), true));
}
if (criteria.getOrganizations() != null && criteria.getOrganizations().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery(Dmp.MapKey.ORGANIZATIONS.getName() + ".id.keyword", criteria.getOrganizations().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getGrantStatus() != null) {
boolQuery = boolQuery.should(QueryBuilders.termQuery(Dmp.MapKey.GRANTSTATUS.getName(), criteria.getGrantStatus()));
}
if (boolQuery.should().isEmpty() && boolQuery.mustNot().isEmpty()) {
boolQuery = boolQuery.should(QueryBuilders.matchAllQuery());
} else {
boolQuery.minimumShouldMatch(boolQuery.should().size());
}
countRequest.query(boolQuery);
CountResponse response = this.getClient().count(countRequest, RequestOptions.DEFAULT);
return response.getCount();
}
return null;
}
public boolean createIndex() {
try {
if (!this.exists()) {

9
dmp-backend/web/src/main/java/eu/eudat/controllers/DMPs.java
View File

@ -243,7 +243,6 @@ public class DMPs extends BaseController {
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<UUID>().status(ApiMessageCode.SUCCESS_MESSAGE).payload(cloneId));
}
@Transactional
@RequestMapping(method = RequestMethod.DELETE, value = {"{id}"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DMP>> delete(@PathVariable UUID id, Principal principal) {
@ -260,7 +259,7 @@ public class DMPs extends BaseController {
if (files[0].getContentType().equals(APPLICATION_JSON.toString())) {
this.dataManagementPlanManager.createFromRDA(files, principal, profiles);
} else if (files[0].getContentType().equals(APPLICATION_ATOM_XML.toString()) || files[0].getContentType().equals(TEXT_XML.toString())) {
this.dataManagementPlanManager.createDmpFromXml(this.getApiContext(), files, principal);
this.dataManagementPlanManager.createDmpFromXml(files, principal, profiles);
} else {
return ResponseEntity.badRequest().body(new ResponseItem().status(ApiMessageCode.ERROR_MESSAGE).message("File format is not supported"));
}
@ -279,7 +278,6 @@ public class DMPs extends BaseController {
}
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/finalize/{id}"})
public ResponseEntity<ResponseItem<DMP>> makeFinalize(@PathVariable String id, Principal principal, @RequestBody DatasetsToBeFinalized datasetsToBeFinalized) {
try {
@ -291,7 +289,6 @@ public class DMPs extends BaseController {
}
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/unfinalize/{id}"})
public ResponseEntity<ResponseItem<DMP>> undoFinalize(@PathVariable String id, Principal principal) {
try {
@ -304,7 +301,6 @@ public class DMPs extends BaseController {
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/updateusers/{id}"})
public ResponseEntity<ResponseItem<DMP>> updateUsers(@PathVariable String id, @RequestBody List<UserInfoListingModel> users, Principal principal) {
try {
@ -320,7 +316,6 @@ public class DMPs extends BaseController {
* DOI Generation
* */
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/createZenodoDoi/{id}"})
public ResponseEntity<ResponseItem<String>> createZenodoDoi(@PathVariable String id, Principal principal) {
try {
@ -328,7 +323,7 @@ public class DMPs extends BaseController {
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Successfully created DOI for Data Datamanagement Plan in question.").payload(zenodoDOI));
} catch (Exception e) {
logger.error(e.getMessage(), e);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create DOI for the Data Management Plan."));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create DOI for the Data Management Plan: " + e.getMessage()));
}
}

6
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DashBoardManager.java
View File

@ -182,14 +182,14 @@ public class DashBoardManager {
.selectAsync(item -> recentActivityDataBuilder.label(item.getLabel()).timestamp(item.getModified()).id(item.getId().toString()).build())
.whenComplete((datasetActivities, throwable) -> activity.setRecentDatasetActivities(datasetActivities));
CompletableFuture<List<RecentActivityData>> grants = grantRepository.getAuthenticated(grantRepository.getWithCriteria(grantCriteria), user)
/*CompletableFuture<List<RecentActivityData>> grants = grantRepository.getAuthenticated(grantRepository.getWithCriteria(grantCriteria), user)
.withHint("grantRecentActivity")
.orderBy((builder, root) -> builder.desc(root.get("modified")))
.take(numberofactivities)
.selectAsync(item -> recentActivityDataBuilder.label(item.getLabel()).timestamp(item.getModified()).id(item.getId().toString()).build())
.whenComplete((grantActivities, throwable) -> activity.setRecentGrantActivities(grantActivities));
.whenComplete((grantActivities, throwable) -> activity.setRecentGrantActivities(grantActivities));*/
CompletableFuture.allOf(grants, dmps, datasets).join();
CompletableFuture.allOf(/*grants, */dmps, datasets).join();
return activity;
}

232
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java
View File

@ -1,5 +1,6 @@
package eu.eudat.logic.managers;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.configurations.dynamicgrant.DynamicGrantConfiguration;
@ -13,6 +14,7 @@ import eu.eudat.data.enumeration.notification.ActiveStatus;
import eu.eudat.data.enumeration.notification.ContactType;
import eu.eudat.data.enumeration.notification.NotificationType;
import eu.eudat.data.enumeration.notification.NotifyState;
import eu.eudat.data.query.items.table.dataset.DatasetTableRequest;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
import eu.eudat.data.query.items.table.dmp.DataManagementPlanTableRequest;
import eu.eudat.elastic.criteria.DmpCriteria;
@ -68,8 +70,6 @@ import org.springframework.core.env.Environment;
import org.springframework.core.io.FileSystemResource;
import org.springframework.http.*;
import org.springframework.stereotype.Component;
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.util.MultiValueMap;
import org.springframework.web.client.HttpClientErrorException;
import org.springframework.web.client.HttpServerErrorException;
import org.springframework.web.client.RestTemplate;
@ -129,73 +129,138 @@ public class DataManagementPlanManager {
List<Dmp> dmps = null;
QueryableList<DMP> items = null;
QueryableList<DMP> authItems = null;
Long totalData = 0L;
if (apiContext.getOperationsContext().getElasticRepository().getDmpRepository() != null) {
DmpCriteria criteria = DmpCriteriaMapper.toElasticCriteria(dataManagementPlanTableRequest.getCriteria());
dmps = apiContext.getOperationsContext().getElasticRepository().getDmpRepository().query(criteria);
if (dmps != null && !dmps.isEmpty()) {
List<Dmp> finalDmps = dmps;
items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().asQueryable().where((builder, root) -> root.get("id").in(finalDmps.stream().map(Dmp::getId).collect(Collectors.toList())));
try {
DmpCriteria criteria = DmpCriteriaMapper.toElasticCriteria(dataManagementPlanTableRequest.getCriteria(), principalID);
criteria.setOffset(dataManagementPlanTableRequest.getOffset());
criteria.setSize(dataManagementPlanTableRequest.getLength());
criteria.setSortCriteria(DmpCriteriaMapper.toElasticSorting(dataManagementPlanTableRequest.getOrderings()));
dmps = apiContext.getOperationsContext().getElasticRepository().getDmpRepository().query(criteria);
if (dmps != null && !dmps.isEmpty()) {
List<Dmp> finalDmps = dmps;
items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().asQueryable().where((builder, root) -> root.get("id").in(finalDmps.stream().map(Dmp::getId).collect(Collectors.toList())));
PaginationManager.applyOrder(items, dataManagementPlanTableRequest);
totalData = apiContext.getOperationsContext().getElasticRepository().getDmpRepository().count(criteria);
}
} catch (Exception ex) {
logger.warn(ex.getMessage(), ex);
items = null;
}
}
if (items == null) {
items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(dataManagementPlanTableRequest.getCriteria());
List<Integer> roles = new LinkedList<>();
if (!dataManagementPlanTableRequest.getCriteria().isOnlyPublic()) {
if (dataManagementPlanTableRequest.getCriteria().getRole() != null)
roles.add(dataManagementPlanTableRequest.getCriteria().getRole());
authItems = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(items, principalID, roles);
} else {
authItems = items;
}
totalData = authItems.count();
items = PaginationManager.applyPaging(authItems, dataManagementPlanTableRequest);
}
List<Integer> roles = new LinkedList<>();
if (!dataManagementPlanTableRequest.getCriteria().isOnlyPublic()) {
if (dataManagementPlanTableRequest.getCriteria().getRole() != null)
roles.add(dataManagementPlanTableRequest.getCriteria().getRole());
authItems = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(items, principalID, roles);
} else {
authItems = items;
}
QueryableList<DMP> pagedItems = PaginationManager.applyPaging(authItems, dataManagementPlanTableRequest);
DataTableData<DataManagementPlanListingModel> dataTable = new DataTableData<>();
CompletableFuture itemsFuture;
if (fieldsGroup.equals("listing")) {
if (!dataManagementPlanTableRequest.getCriteria().isOnlyPublic()) {
itemsFuture = pagedItems.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.distinct()
.selectAsync(item -> {
List<DMP> dmps1 = items.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.distinct().toList();
dataTable.setData(dmps1.stream().map(dmp -> {
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(Collections.singletonList(dmp.getId()));
dmp.setDataset(retrieveRelevantDatasets(datasetCriteria, principalID));
return new DataManagementPlanListingModel().fromDataModelDatasets(dmp);
}).collect(Collectors.toList()));
/*.selectAsync(item -> {
item.setDataset(
item.getDataset().stream()
.filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue())).collect(Collectors.toList()).stream()
.filter(dataset -> dataset.getDmp().getUsers().stream()
*//*.filter(dataset -> dataset.getDmp().getUsers().stream()
.filter(x -> x.getUser().getId().equals(principalID))
.collect(Collectors.toList()).size() > 0)
.collect(Collectors.toList()).size() > 0)*//*
.collect(Collectors.toSet()));
return new DataManagementPlanListingModel().fromDataModelDatasets(item);
})
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));*/
} else {
itemsFuture = pagedItems.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.distinct()
.selectAsync(item -> {
List<DMP> dmps1 = items.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.distinct().toList();
dataTable.setData(dmps1.stream().map(dmp -> {
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(Collections.singletonList(dmp.getId()));
datasetCriteria.setIsPublic(true);
dmp.setDataset(retrieveRelevantDatasets(datasetCriteria));
return new DataManagementPlanListingModel().fromDataModelDatasets(dmp);
}).collect(Collectors.toList()));
/*.selectAsync(item -> {
item.setDataset(
item.getDataset().stream()
.filter(dataset -> dataset.getStatus().equals(Dataset.Status.FINALISED.getValue())).collect(Collectors.toSet()));
return new DataManagementPlanListingModel().fromDataModelDatasets(item);
})
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));*/
}
} else if (fieldsGroup.equals("autocomplete")) {
itemsFuture = pagedItems
dataTable.setData(items
.distinct()
.selectAsync(item -> new DataManagementPlanListingModel().fromDataModelAutoComplete(item))
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
.select(item -> new DataManagementPlanListingModel().fromDataModelAutoComplete(item)));
} else {
itemsFuture = pagedItems
dataTable.setData(items
.distinct()
.selectAsync(item -> new DataManagementPlanListingModel().fromDataModelAssociatedProfiles(item))
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
.select(item -> new DataManagementPlanListingModel().fromDataModelAssociatedProfiles(item)));
}
CompletableFuture countFuture = authItems.distinct().countAsync().whenComplete((count, throwable) -> dataTable.setTotalCount(count));
CompletableFuture.allOf(itemsFuture, countFuture).join();
//CompletableFuture countFuture = authItems.distinct().countAsync().whenComplete((count, throwable) -> dataTable.setTotalCount(count));
dataTable.setTotalCount(totalData);
//CompletableFuture.allOf(itemsFuture).join();
return dataTable;
}
private Set<Dataset> retrieveRelevantDatasets(DatasetCriteria datasetCriteria) {
return retrieveRelevantDatasets(datasetCriteria, null);
}
private Set<Dataset> retrieveRelevantDatasets (DatasetCriteria datasetCriteria, UUID principal) {
QueryableList<Dataset> datasetItems = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().getWithCriteria(datasetCriteria);
if (principal != null) {
UserInfo userInfo = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal);
List<Integer> roles = new ArrayList<>();
roles.add(0);
roles.add(1);
datasetItems = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().getAuthenticated(datasetItems, userInfo, roles);
}
Long maxDatasets = datasetItems.count();
DatasetTableRequest datasetTableRequest = new DatasetTableRequest();
datasetTableRequest.setOffset(0);
datasetTableRequest.setLength(3);
Set<Dataset> datasetsSet = new LinkedHashSet<>();
try {
datasetItems = PaginationManager.applyPaging(datasetItems, datasetTableRequest);
List<Dataset> datasets = datasetItems.toList();
datasetsSet.addAll(datasets);
for (int i = 0; i < maxDatasets - datasets.size(); i++) {
Dataset fakedataset = new Dataset();
fakedataset.setId(UUID.randomUUID());
datasetsSet.add(fakedataset);
}
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
return datasetsSet;
}
public eu.eudat.models.data.dmp.DataManagementPlan getSingle(String id, Principal principal, boolean isPublic) throws Exception {
eu.eudat.models.data.dmp.DataManagementPlan dataManagementPlan = new eu.eudat.models.data.dmp.DataManagementPlan();
DMP dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
@ -567,6 +632,16 @@ public class DataManagementPlanManager {
copyDatasets(newDmp, databaseRepository.getDatasetDao());
databaseRepository
.getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), oldDmp.getId()))
.toList().stream().forEach(userDMP -> {
UserDMP temp = new UserDMP();
temp.setUser(userDMP.getUser());
temp.setRole(userDMP.getRole());
temp.setDmp(newDmp);
apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().createOrUpdate(temp);
});
newDmp.setUsers(new HashSet<>(databaseRepository.getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), newDmp.getId())).toList()));
DatasetCriteria criteria1 = new DatasetCriteria();
@ -859,6 +934,7 @@ public class DataManagementPlanManager {
datasetElastic.setCollaborators(dataset1.getDmp().getUsers().stream().map(user -> {
Collaborator collaborator = new Collaborator();
collaborator.setId(user.getId().toString());
collaborator.setRole(user.getRole());
// collaborator.setName(user.getUser().getName());
return collaborator;
}).collect(Collectors.toList()));
@ -1192,7 +1268,7 @@ public class DataManagementPlanManager {
if (versioned) {
fileName += "_" + dmpEntity.getVersion();
}
fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
// fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
FileEnvelope exportEnvelope = new FileEnvelope();
exportEnvelope.setFilename(fileName + ".docx");
String uuid = UUID.randomUUID().toString();
@ -1226,6 +1302,22 @@ public class DataManagementPlanManager {
dmpName.setTextContent(dmp.getLabel());
dmpElement.appendChild(dmpName);
if (dmp.getExtraProperties() != null && !dmp.getExtraProperties().isEmpty()) {
Map<String, Object> extraProperties = new ObjectMapper().readValue(dmp.getExtraProperties(), HashMap.class);
Element language = xmlDoc.createElement("language");
language.setTextContent(extraProperties.get("language") != null ? extraProperties.get("language").toString() : null);
dmpElement.appendChild(language);
Element visibility = xmlDoc.createElement("visibility");
visibility.setTextContent(extraProperties.get("visible") != null ? extraProperties.get("visible").toString() : null);
dmpElement.appendChild(visibility);
Element publicDate = xmlDoc.createElement("publicDate");
publicDate.setTextContent(extraProperties.get("publicDate") != null ? extraProperties.get("publicDate").toString() : null);
dmpElement.appendChild(publicDate);
Element costs = xmlDoc.createElement("costs");
costs.setTextContent(extraProperties.get("costs") != null ? extraProperties.get("costs").toString() : null);
dmpElement.appendChild(costs);
}
DMPProfile dmpProfile = dmp.getProfile();
Element dmpProfileElement = xmlDoc.createElement("dmpProfile");
Element dmpProfileName = xmlDoc.createElement("dmpProfileName");
@ -1341,7 +1433,7 @@ public class DataManagementPlanManager {
return fileEnvelope;
}
public ResponseEntity<byte[]> getRDAJsonDocument(String id, DatasetManager datasetManager, Principal principal) throws IOException {
public ResponseEntity<byte[]> getRDAJsonDocument(String id, DatasetManager datasetManager, Principal principal) throws Exception {
eu.eudat.data.entities.DMP dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (!dmp.isPublic() && dmp.getUsers().stream().noneMatch(userInfo -> userInfo.getUser().getId() == principal.getId()))
throw new UnauthorisedException();
@ -1410,7 +1502,7 @@ public class DataManagementPlanManager {
* Data Import
* */
public List<DmpImportModel> createDmpFromXml(ApiContext apiContext, MultipartFile[] files, Principal principal) throws IOException, JAXBException, Exception {
public List<DmpImportModel> createDmpFromXml(MultipartFile[] files, Principal principal, String[] profiles) throws IOException, JAXBException, Exception {
List<DmpImportModel> dataManagementPlans = new ArrayList<>();
// Jaxb approach.
JAXBContext jaxbContext;
@ -1466,16 +1558,26 @@ public class DataManagementPlanManager {
projectEditor.setExistProject(project);
List<eu.eudat.models.data.dmp.AssociatedProfile> associatedProfiles = new LinkedList<>();
if (profiles != null && profiles.length > 0) {
for (String profile : profiles) {
DatasetProfile exProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(profile));
AssociatedProfile associatedProfile = new AssociatedProfile().fromData(exProfile);
associatedProfiles.add(associatedProfile);
}
}
for (AssociatedProfileImportModels a : dataManagementPlans.get(0).getProfilesImportModels()) {
AssociatedProfile associatedProfile = new AssociatedProfile();
associatedProfile.setId(a.getId());
associatedProfile.setLabel(a.getLabel());
associatedProfiles.add(associatedProfile);
try {
DatasetProfile exProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(a.getId());
AssociatedProfile associatedProfile = new AssociatedProfile().fromData(exProfile);
associatedProfiles.add(associatedProfile);
} catch (Exception ignored) {
}
}
List<eu.eudat.models.data.dmp.Organisation> organisations = new ArrayList<>();
for (OrganisationImportModel org : dataManagementPlans.get(0).getOrganisationImportModels()) {
eu.eudat.models.data.dmp.Organisation organisation = new eu.eudat.models.data.dmp.Organisation();
organisation.setLabel(org.getOrganaisationNameImport());
organisation.setName(org.getOrganaisationNameImport());
organisation.setReference(org.getOrganaisationReferenceImport());
organisation.setKey(organisation.getReference().split(":")[0]);
organisations.add(organisation);
@ -1504,6 +1606,21 @@ public class DataManagementPlanManager {
dm.setAssociatedUsers(associatedUsers); // Sets associatedUsers property.
dm.setDynamicFields(dynamicFields); // Sets dynamicFields property.
dm.setDefinition(dmpProfile);
ObjectMapper mapper = new ObjectMapper();
Map<String, Object> extraPropertiesMap = new HashMap<>();
if (dataManagementPlans.get(0).getLanguage() != null) {
extraPropertiesMap.put("language", dataManagementPlans.get(0).getLanguage());
}
if (dataManagementPlans.get(0).getVisibility() != null) {
extraPropertiesMap.put("visible", dataManagementPlans.get(0).getVisibility());
}
if (dataManagementPlans.get(0).getPublicDate() != null) {
extraPropertiesMap.put("publicDate", dataManagementPlans.get(0).getPublicDate());
}
if (dataManagementPlans.get(0).getCosts() != null) {
extraPropertiesMap.put("costs", mapper.readValue(dataManagementPlans.get(0).getCosts(), ArrayList.class));
}
dm.setExtraProperties(extraPropertiesMap);
//createOrUpdate(apiContext, dm, principal);
DMP dmp = this.createOrUpdate(dm, principal);
@ -1527,7 +1644,11 @@ public class DataManagementPlanManager {
for (DatasetImportModels das: dataManagementPlans.get(0).getDatasetImportModels()) {
eu.eudat.data.entities.Dataset dataset = new eu.eudat.data.entities.Dataset();
dataset.setLabel(das.getName());
dataset.setProfile(databaseRepository.getDatasetProfileDao().find(das.getProfile()));
try {
dataset.setProfile(databaseRepository.getDatasetProfileDao().find(das.getProfile()));
} catch (Exception ignored) {
dataset.setProfile(databaseRepository.getDatasetProfileDao().find(associatedProfiles.get(0).getId()));
}
dataset.setProperties(new ObjectMapper().writeValueAsString(das.getFieldImportModels()));
dataset.setStatus((short) 0);
dataset.setRegistries(new HashSet<>());
@ -1749,7 +1870,7 @@ public class DataManagementPlanManager {
}
private boolean isUserOwnerOfDmp(DMP dmp, Principal principal) {
return (dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getId()).equals(principal.getId());
return (dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).map(userDMP -> userDMP.getUser().getId())).collect(Collectors.toList()).contains(principal.getId());
}
/*
@ -1906,6 +2027,9 @@ public class DataManagementPlanManager {
i++;
}
dataBuilder.append("],\n");
if (dmp.getGrant().getReference() == null) {
dmp.getGrant().setReference("dmp:" + dmp.getGrant().getId());
}
String grantReferenceHead = dmp.getGrant().getReference().split(":")[0];
if (grantReferenceHead.equals("openaire")) {
String grantReferenceTail = dmp.getGrant().getReference().split(":")[3];
@ -1914,6 +2038,7 @@ public class DataManagementPlanManager {
dataBuilder.append(" \"grants\": [{\n");
dataBuilder.append(" \t\t\"id\": \"").append(finalId).append("\"\n}],\n");
}
dataBuilder.append(" \"creators\": [{\n");
dataBuilder.append(" \t\t\"name\": \"").append(dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getName()).append("\",\n");
if (dmp.getOrganisations() != null && !dmp.getOrganisations().isEmpty()) {
@ -1932,7 +2057,9 @@ public class DataManagementPlanManager {
}
dataBuilder.append(" }\n").append("}");
createData = dataBuilder.toString();
JsonNode createDataJSON = new ObjectMapper().readTree(createData);
ObjectMapper mapper = new ObjectMapper();
mapper.configure(JsonParser.Feature.ALLOW_UNQUOTED_CONTROL_CHARS, true);
JsonNode createDataJSON = mapper.readTree(createData);
HttpEntity<JsonNode> request = new HttpEntity<>(createDataJSON, headers);
Map createResponse = null;
LinkedHashMap<String, String> links = null;
@ -1995,17 +2122,22 @@ public class DataManagementPlanManager {
if (unpublishedUrl == null) {
// Second step, add the file to the entry.
FileEnvelope file = getWordDocument(id.toString(), principal, configLoader);
/*String name = file.getFilename().substring(0, file.getFilename().length() - 5);
String name = file.getFilename().substring(0, file.getFilename().length() - 5);
File pdfFile = datasetManager.convertToPDF(file, environment);
String fileName = name + ".pdf";*/
FileSystemResource fileSystemResource = new FileSystemResource(file.getFile());
String fileName = name + ".pdf";
FileSystemResource fileSystemResource = new FileSystemResource(pdfFile);
HttpEntity<FileSystemResource> addFileMapRequest = new HttpEntity<>(fileSystemResource, null);
String addFileUrl = links.get("bucket") + "/" + file.getFilename() + "?access_token=" + zenodoToken;
String addFileUrl = links.get("bucket") + "/" + fileName + "?access_token=" + zenodoToken;
restTemplate.put(addFileUrl, addFileMapRequest);
Files.deleteIfExists(file.getFile().toPath());
ResponseEntity<byte[]> jsonFile = getRDAJsonDocument(id.toString(), datasetManager, principal);
ResponseEntity<byte[]> jsonFile;
try {
jsonFile = getRDAJsonDocument(id.toString(), datasetManager, principal);
} catch (Exception e) {
throw e;
}
UUID jsonFileUUID = UUID.randomUUID();
File tempJsonFile = new File(this.environment.getProperty("temp.temp") + jsonFileUUID.toString() + ".json");
try (FileOutputStream jsonFos = new FileOutputStream(tempJsonFile)) {

26
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java
View File

@ -22,6 +22,7 @@ import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.builders.BuilderFactory;
import eu.eudat.logic.builders.entity.UserInfoBuilder;
import eu.eudat.logic.mapper.elastic.DatasetMapper;
import eu.eudat.logic.mapper.elastic.criteria.DmpCriteriaMapper;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.forms.VisibilityRuleService;
@ -137,9 +138,21 @@ public class DatasetManager {
if (datasetTableRequest.getCriteria().getIsPublic() != null) {
datasetCriteria.setPublic(datasetTableRequest.getCriteria().getIsPublic());
}
if (!datasetCriteria.isPublic()) {
if (datasetCriteria.getCollaborators() == null) {
datasetCriteria.setSortCriteria(new ArrayList<>());
}
datasetCriteria.getCollaborators().add(principal.getId());
}
if (datasetTableRequest.getCriteria().getGrantStatus() != null) {
datasetCriteria.setGrantStatus(datasetTableRequest.getCriteria().getGrantStatus());
}
if (datasetTableRequest.getOrderings() != null) {
datasetCriteria.setSortCriteria(DmpCriteriaMapper.toElasticSorting(datasetTableRequest.getOrderings()));
}
datasetCriteria.setOffset(datasetTableRequest.getOffset());
datasetCriteria.setSize(datasetTableRequest.getLength());
List<eu.eudat.elastic.entities.Dataset> datasets;
try {
datasets = datasetRepository.exists() ?
@ -206,6 +219,11 @@ public class DatasetManager {
datasetCriteria.setDatasetTemplates(datasetTableRequest.getCriteria().getDatasetProfile());
datasetCriteria.setDmps(datasetTableRequest.getCriteria().getDmpIds());
datasetCriteria.setGrants(datasetTableRequest.getCriteria().getGrants());
if (datasetTableRequest.getOrderings() != null) {
datasetCriteria.setSortCriteria(DmpCriteriaMapper.toElasticSorting(datasetTableRequest.getOrderings()));
}
datasetCriteria.setOffset(datasetTableRequest.getOffset());
datasetCriteria.setSize(datasetTableRequest.getLength());
List<eu.eudat.elastic.entities.Dataset> datasets;
try {
datasets = datasetRepository.exists() ?
@ -214,9 +232,9 @@ public class DatasetManager {
logger.warn(ex.getMessage());
datasets = null;
}
datasetTableRequest.setQuery(databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class)));
QueryableList<Dataset> items = datasetTableRequest.applyCriteria();
/*QueryableList<Dataset> items;
/*datasetTableRequest.setQuery(databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class)));
QueryableList<Dataset> items = datasetTableRequest.applyCriteria();*/
QueryableList<Dataset> items;
if (datasets != null) {
if (!datasets.isEmpty()) {
items = databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class));
@ -227,7 +245,7 @@ public class DatasetManager {
items.where((builder, root) -> root.get("id").in(new UUID[]{UUID.randomUUID()}));
} else {
items = datasetTableRequest.applyCriteria();
}*/
}
if (principal.getId() != null && datasetTableRequest.getCriteria().getRole() != null) {
items.where((builder, root) -> {

3
dmp-backend/web/src/main/java/eu/eudat/logic/mapper/elastic/CollaboratorMapper.java
View File

@ -5,10 +5,11 @@ import eu.eudat.elastic.entities.Collaborator;
public class CollaboratorMapper {
public static Collaborator toElastic(UserInfo user) {
public static Collaborator toElastic(UserInfo user, Integer role) {
Collaborator elastic = new Collaborator();
elastic.setId(user.getId().toString());
elastic.setName(user.getName());
elastic.setRole(role);
return elastic;
}
}

5
dmp-backend/web/src/main/java/eu/eudat/logic/mapper/elastic/DatasetMapper.java
View File

@ -50,8 +50,11 @@ public class DatasetMapper {
elastic.setDmp(dataset.getDmp().getId());
elastic.setGroup(dataset.getDmp().getGroupId());
elastic.setGrant(dataset.getDmp().getGrant().getId());
elastic.setCreated(dataset.getCreated());
elastic.setModified(dataset.getModified());
elastic.setFinalizedAt(dataset.getFinalizedAt());
if (dataset.getDmp().getUsers() != null) {
elastic.setCollaborators(dataset.getDmp().getUsers().stream().map(user -> CollaboratorMapper.toElastic(user.getUser())).collect(Collectors.toList()));
elastic.setCollaborators(dataset.getDmp().getUsers().stream().map(user -> CollaboratorMapper.toElastic(user.getUser(), user.getRole())).collect(Collectors.toList()));
}
DataManagementPlanCriteria dmpCriteria = new DataManagementPlanCriteria();
dmpCriteria.setAllVersions(true);

6
dmp-backend/web/src/main/java/eu/eudat/logic/mapper/elastic/DmpMapper.java
View File

@ -34,13 +34,17 @@ public class DmpMapper {
elastic.setId(dmp.getId());
elastic.setGroupId(dmp.getGroupId());
if (dmp.getUsers() != null) {
elastic.setCollaborators(dmp.getUsers().stream().map(user -> CollaboratorMapper.toElastic(user.getUser())).collect(Collectors.toList()));
elastic.setCollaborators(dmp.getUsers().stream().map(user -> CollaboratorMapper.toElastic(user.getUser(), user.getRole())).collect(Collectors.toList()));
}
elastic.setDescription(dmp.getDescription());
elastic.setGrant(dmp.getGrant().getId());
elastic.setLabel(dmp.getLabel());
elastic.setPublic(dmp.isPublic());
elastic.setStatus(dmp.getStatus());
elastic.setCreated(dmp.getCreated());
elastic.setModified(dmp.getModified());
elastic.setFinalizedAt(dmp.getFinalizedAt());
elastic.setPublishedAt(dmp.getPublishedAt());
DataManagementPlanCriteria dmpCriteria = new DataManagementPlanCriteria();
dmpCriteria.setAllVersions(true);
dmpCriteria.setGroupIds(Collections.singletonList(dmp.getGroupId()));

28
dmp-backend/web/src/main/java/eu/eudat/logic/mapper/elastic/criteria/DmpCriteriaMapper.java
View File

@ -2,14 +2,20 @@ package eu.eudat.logic.mapper.elastic.criteria;
import eu.eudat.data.dao.criteria.DataManagementPlanCriteria;
import eu.eudat.data.entities.Grant;
import eu.eudat.data.query.definition.helpers.ColumnOrderings;
import eu.eudat.data.query.definition.helpers.Ordering;
import eu.eudat.elastic.criteria.DmpCriteria;
import eu.eudat.elastic.criteria.SortCriteria;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
public class DmpCriteriaMapper {
public static DmpCriteria toElasticCriteria(DataManagementPlanCriteria criteria) {
public static DmpCriteria toElasticCriteria(DataManagementPlanCriteria criteria, UUID principalID) {
DmpCriteria elastic = new DmpCriteria();
elastic.setAllowAllVersions(criteria.getAllVersions());
@ -23,6 +29,12 @@ public class DmpCriteriaMapper {
elastic.setOrganizations(criteria.getOrganisations().stream().map(UUID::fromString).collect(Collectors.toList()));
}
elastic.setPublic(criteria.getIsPublic());
if (!elastic.isPublic()) {
elastic.setCollaborators(Collections.singletonList(principalID));
}
if (criteria.getRole() != null) {
elastic.setRoles(Collections.singletonList(criteria.getRole()));
}
if (criteria.getStatus() != null) {
elastic.setStatus(criteria.getStatus().shortValue());
}
@ -30,4 +42,18 @@ public class DmpCriteriaMapper {
elastic.setGrantStatus(criteria.getGrantStatus());
return elastic;
}
public static List<SortCriteria> toElasticSorting(ColumnOrderings columnOrderings) {
List<SortCriteria> sortCriteria = new ArrayList<>();
if (columnOrderings.getFieldOrderings() != null && columnOrderings.getFieldOrderings().length > 0) {
for (Ordering ordering: columnOrderings.getFieldOrderings()) {
SortCriteria sortCriteria1 = new SortCriteria();
sortCriteria1.setFieldName(ordering.getFieldName() + (ordering.getFieldName().contains("label") ?".keyword" : ""));
sortCriteria1.setColumnType(ordering.getColumnType() != null ? SortCriteria.ColumnType.valueOf(ordering.getColumnType().name()): SortCriteria.ColumnType.COLUMN);
sortCriteria1.setOrderByType(SortCriteria.OrderByType.valueOf(ordering.getOrderByType().name()));
sortCriteria.add(sortCriteria1);
}
}
return sortCriteria;
}
}

89
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/word/WordBuilder.java
View File

@ -144,67 +144,89 @@ public class WordBuilder {
private void createSections(List<Section> sections, XWPFDocument mainDocumentPart, ParagraphStyle style, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService, Integer page, String sectionString) {
if (createListing) this.addListing(mainDocumentPart, indent, false, true);
sections.forEach(section -> {
boolean hasValue = false;
for (Section section: sections) {
int paragraphPos = -1;
String tempSectionString = sectionString != null ? sectionString + "." + (section.getOrdinal() + 1) : "" + (section.getOrdinal() + 1);
if (visibilityRuleService.isElementVisible(section.getId())) {
if (!createListing) {
XWPFParagraph paragraph = addParagraphContent(page + "." + tempSectionString + " " + section.getTitle(), mainDocumentPart, style, numId);
CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
number.setVal(BigInteger.valueOf(indent));
paragraphPos = mainDocumentPart.getPosOfParagraph(paragraph);
}
createSections(section.getSections(), mainDocumentPart, ParagraphStyle.HEADER5, 1, createListing, visibilityRuleService, page, tempSectionString);
createCompositeFields(section.getCompositeFields(), mainDocumentPart, 2, createListing, visibilityRuleService, page, tempSectionString);
hasValue = createCompositeFields(section.getCompositeFields(), mainDocumentPart, 2, createListing, visibilityRuleService, page, tempSectionString);
if (!hasValue && paragraphPos > -1) {
mainDocumentPart.removeBodyElement(paragraphPos);
}
}
});
}
}
private void createCompositeFields(List<FieldSet> compositeFields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService, Integer page, String section) {
private Boolean createCompositeFields(List<FieldSet> compositeFields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService, Integer page, String section) {
if (createListing) this.addListing(mainDocumentPart, indent, true, true);
compositeFields.forEach(compositeField -> {
boolean hasValue = false;
for (FieldSet compositeField: compositeFields) {
if (visibilityRuleService.isElementVisible(compositeField.getId()) && hasVisibleFields(compositeField, visibilityRuleService)) {
int paragraphPos = -1;
if (compositeField.getTitle() != null && !compositeField.getTitle().isEmpty() && !createListing) {
XWPFParagraph paragraph = addParagraphContent(page + "." + section + "." + (compositeField.getOrdinal() +1) + " " + compositeField.getTitle(), mainDocumentPart, ParagraphStyle.HEADER6, numId);
CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
number.setVal(BigInteger.valueOf(indent));
paragraphPos = mainDocumentPart.getPosOfParagraph(paragraph);
}
createFields(compositeField.getFields(), mainDocumentPart, 3, createListing, visibilityRuleService);
hasValue = createFields(compositeField.getFields(), mainDocumentPart, 3, createListing, visibilityRuleService);
if (compositeField.getMultiplicityItems() != null && !compositeField.getMultiplicityItems().isEmpty()) {
for (FieldSet multiplicityFieldset : compositeField.getMultiplicityItems()) {
createFields(multiplicityFieldset.getFields(), mainDocumentPart, 3, createListing, visibilityRuleService);
hasValue = createFields(multiplicityFieldset.getFields(), mainDocumentPart, 3, createListing, visibilityRuleService);
}
}
if (compositeField.getHasCommentField() && compositeField.getCommentFieldValue() != null && !compositeField.getCommentFieldValue().isEmpty() && !createListing) {
if (hasValue && compositeField.getHasCommentField() && compositeField.getCommentFieldValue() != null && !compositeField.getCommentFieldValue().isEmpty() && !createListing) {
XWPFParagraph paragraph = addParagraphContent("Comment: " + compositeField.getCommentFieldValue(), mainDocumentPart, ParagraphStyle.COMMENT, numId);
CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
number.setVal(BigInteger.valueOf(indent));
}
if (!hasValue && paragraphPos > -1) {
mainDocumentPart.removeBodyElement(paragraphPos);
}
}
});
}
return hasValue;
}
private void createFields(List<Field> fields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
private Boolean createFields(List<Field> fields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
if (createListing) this.addListing(mainDocumentPart, indent, false, false);
fields.forEach(field -> {
boolean hasValue = false;
for (Field field: fields) {
if (visibilityRuleService.isElementVisible(field.getId())) {
if (!createListing) {
try {
XWPFParagraph paragraph = addParagraphContent(this.formatter(field), mainDocumentPart, ParagraphStyle.TEXT, numId);
CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
number.setVal(BigInteger.valueOf(indent));
if (paragraph != null) {
CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
number.setVal(BigInteger.valueOf(indent));
hasValue = true;
}
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
}
}
});
}
return hasValue;
}
public XWPFParagraph addParagraphContent(String text, XWPFDocument mainDocumentPart, ParagraphStyle style, BigInteger numId) {
XWPFParagraph paragraph = this.options.get(style).apply(mainDocumentPart, text);
if (numId != null) {
paragraph.setNumID(numId);
if (text != null && !text.isEmpty()) {
XWPFParagraph paragraph = this.options.get(style).apply(mainDocumentPart, text);
if (numId != null) {
paragraph.setNumID(numId);
}
return paragraph;
}
return paragraph;
return null;
}
private void addListing(XWPFDocument document, int indent, Boolean question, Boolean hasIndication) {
@ -254,6 +276,7 @@ public class WordBuilder {
mapList = Arrays.asList(mapper.readValue(field.getValue().toString(), HashMap[].class));
}catch (Exception e) {
logger.warn(e.getMessage(), e);
logger.info("Moving to fallback parsing");
Map <String, Object> map = new HashMap<>();
map.put("label", field.getValue().toString());
mapList.add(map);
@ -304,6 +327,7 @@ public class WordBuilder {
WordListData wordListData = (WordListData) field.getData();
if (wordListData.getOptions().isEmpty() && field.getValue() != null) {
logger.warn("World List has no values but the field has");
logger.info("Return value as is");
return field.getValue().toString();
} else if (field.getValue() != null){
ComboBoxData<WordListData>.Option selectedOption = null;
@ -332,21 +356,24 @@ public class WordBuilder {
return field.getValue() != null ? field.getValue().toString(): "";
case "datasetIdentifier":
case "validation":
Map<String, String> identifierData;
try {
ObjectMapper mapper = new ObjectMapper();
identifierData = mapper.readValue(field.getValue().toString(), HashMap.class);
} catch (JsonParseException ex) {
identifierData = new HashMap<>();
String parsedData = field.getValue().toString().substring(1, field.getValue().toString().length() - 1);
StringTokenizer commaTokens = new StringTokenizer(parsedData, ", ");
while (commaTokens.hasMoreTokens()) {
String token = commaTokens.nextToken();
StringTokenizer equalTokens = new StringTokenizer(token, "=");
identifierData.put(equalTokens.nextToken(), equalTokens.nextToken());
if (field.getValue() != null) {
Map<String, String> identifierData;
try {
ObjectMapper mapper = new ObjectMapper();
identifierData = mapper.readValue(field.getValue().toString(), HashMap.class);
} catch (JsonParseException ex) {
identifierData = new HashMap<>();
String parsedData = field.getValue().toString().substring(1, field.getValue().toString().length() - 1);
StringTokenizer commaTokens = new StringTokenizer(parsedData, ", ");
while (commaTokens.hasMoreTokens()) {
String token = commaTokens.nextToken();
StringTokenizer equalTokens = new StringTokenizer(token, "=");
identifierData.put(equalTokens.nextToken(), equalTokens.nextToken());
}
}
return "id: " + identifierData.get("identifier") + ", Validation Type: " + identifierData.get("type");
}
return "id: " + identifierData.get("identifier") + ", Validation Type: " + identifierData.get("type");
return "";
}
return null;
}

37
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DmpImportModel.java
View File

@ -19,6 +19,10 @@ public class DmpImportModel {
private List<UserInfoImportModels> associatedUsersImportModels;
private List<DynamicFieldWithValueImportModels> dynamicFieldsImportModels;
private List<DatasetImportModels> datasetImportModels;
private String language;
private Boolean visibility;
private String publicDate;
private String costs;
@XmlElement(name = "description")
public String getDescriptionImport() {
@ -113,4 +117,37 @@ public class DmpImportModel {
@XmlElement(name = "dataset")
public List<DatasetImportModels> getDatasetImportModels() { return datasetImportModels; }
public void setDatasetImportModels(List<DatasetImportModels> datasetImportModels) { this.datasetImportModels = datasetImportModels; }
@XmlElement(name = "language")
public String getLanguage() {
return language;
}
public void setLanguage(String language) {
this.language = language;
}
@XmlElement(name = "visibility")
public Boolean getVisibility() {
return visibility;
}
public void setVisibility(Boolean visibility) {
this.visibility = visibility;
}
@XmlElement(name = "publicDate")
public String getPublicDate() {
return publicDate;
}
public void setPublicDate(String publicDate) {
this.publicDate = publicDate;
}
@XmlElement(name = "costs")
public String getCosts() {
return costs;
}
public void setCosts(String costs) {
this.costs = costs;
}
}

56
dmp-backend/web/src/main/java/eu/eudat/models/data/listingmodels/DataManagementPlanListingModel.java
View File

@ -24,19 +24,19 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
private String id;
private String label;
private String grant;
private String profile;
private Date creationTime;
// private String profile;
// private Date creationTime;
private Date modifiedTime;
private String organisations;
//private String organisations;
private int version;
private int status;
private UUID groupId;
private List<DatasetUrlListing> datasets;
private List<AssociatedProfile> associatedProfiles;
// private List<AssociatedProfile> associatedProfiles;
private List<UserInfoListingModel> users;
private String description;
private String grantAbbreviation;
private String grantId;
// private String grantAbbreviation;
// private String grantId;
private Date finalizedAt;
private Boolean isPublic;
private Date publishedAt;
@ -63,19 +63,19 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
this.grant = grant;
}
public String getProfile() {
/* public String getProfile() {
return profile;
}
public void setProfile(String profile) {
this.profile = profile;
}
}*/
public Date getCreationTime() {
/*public Date getCreationTime() {
return creationTime;
}
public void setCreationTime(Date creationTime) {
this.creationTime = creationTime;
}
}*/
public Date getModifiedTime() {
return modifiedTime;
@ -84,12 +84,12 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
this.modifiedTime = modifiedTime;
}
public String getOrganisations() {
/*public String getOrganisations() {
return organisations;
}
public void setOrganisations(String organisations) {
this.organisations = organisations;
}
}*/
public int getVersion() {
return version;
@ -119,12 +119,12 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
this.status = status;
}
public List<AssociatedProfile> getAssociatedProfiles() {
/*public List<AssociatedProfile> getAssociatedProfiles() {
return associatedProfiles;
}
public void setAssociatedProfiles(List<AssociatedProfile> associatedProfiles) {
this.associatedProfiles = associatedProfiles;
}
}*/
public List<UserInfoListingModel> getUsers() {
return users;
@ -140,19 +140,19 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
this.description = description;
}
public String getGrantAbbreviation() {
/*public String getGrantAbbreviation() {
return grantAbbreviation;
}
public void setGrantAbbreviation(String grantAbbreviation) {
this.grantAbbreviation = grantAbbreviation;
}
}*/
public String getGrantId() {
/*public String getGrantId() {
return grantId;
}
public void setGrantId(String grantId) {
this.grantId = grantId;
}
}*/
public Date getFinalizedAt() {
return finalizedAt;
@ -187,8 +187,8 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
this.id = entity.getId().toString();
this.label = entity.getLabel();
this.groupId = entity.getGroupId();
this.creationTime = entity.getCreated();
this.associatedProfiles = entity.getAssociatedDmps().stream().map(item -> new AssociatedProfile().fromData(item)).collect(Collectors.toList());
// this.creationTime = entity.getCreated();
// this.associatedProfiles = entity.getAssociatedDmps().stream().map(item -> new AssociatedProfile().fromData(item)).collect(Collectors.toList());
return this;
}
@ -196,7 +196,7 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
this.id = entity.getId().toString();
this.label = entity.getLabel();
this.groupId = entity.getGroupId();
this.creationTime = entity.getCreated();
// this.creationTime = entity.getCreated();
return this;
}
@ -205,26 +205,26 @@ public class DataManagementPlanListingModel implements DataModel<DMP, DataManage
this.status = entity.getStatus();
this.version = entity.getVersion();
this.grant = entity.getGrant().getLabel();
if (entity.getProfile() != null) this.profile = entity.getProfile().getLabel();
this.creationTime = entity.getCreated();
/*if (entity.getProfile() != null) this.profile = entity.getProfile().getLabel();
this.creationTime = entity.getCreated();*/
this.modifiedTime = entity.getModified();
this.organisations = LabelBuilder.getLabel(entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()));
// this.organisations = LabelBuilder.getLabel(entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()));
this.datasets = entity.getDataset().stream().map(x-> new DatasetUrlListing().fromDataModel(x)).collect(Collectors.toList());
this.users = entity.getUsers().stream().map(x -> new UserInfoListingModel().fromDataModel(x)).collect(Collectors.toList());
this.description = entity.getDescription();
this.grantAbbreviation = entity.getGrant().getAbbreviation();
this.grantId = entity.getGrant().getId().toString();
// this.grantAbbreviation = entity.getGrant().getAbbreviation();
// this.grantId = entity.getGrant().getId().toString();
this.finalizedAt = entity.getFinalizedAt();
this.isPublic = entity.isPublic();
this.publishedAt = entity.getPublishedAt();
if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
/*if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
this.associatedProfiles = new LinkedList<>();
for (DatasetProfile datasetProfile: entity.getAssociatedDmps()) {
AssociatedProfile associatedProfile = new AssociatedProfile().fromData(datasetProfile);
this.associatedProfiles.add(associatedProfile);
}
}
}*/
return this;
}

2
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/DatasetRDAMapper.java
View File

@ -108,7 +108,7 @@ public class DatasetRDAMapper {
for (int i = 0; i < keywordNodes.size(); i++) {
rda.setAdditionalProperty("keyword" + (i + 1), keywordNodes.get(i).get("id").asText());
}
} else {
} else if (apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().exists()) {
List<String> tags = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(dataset.getId().toString()).getTags().stream().map(Tag::getName).collect(Collectors.toList());
rda.setKeyword(tags);
}

2
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/DmpRDAMapper.java
View File

@ -36,7 +36,7 @@ public class DmpRDAMapper {
}
Map<String, Object> extraProperties;
if (dmp.getExtraProperties() == null) {
throw new IllegalArgumentException("DMP is missing required Data for RDA export");
throw new IllegalArgumentException("DMP is missing language and contact properties");
} else {
extraProperties = new org.json.JSONObject(dmp.getExtraProperties()).toMap();
if (extraProperties.get("language") == null) {

12
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/FundingRDAMapper.java
View File

@ -6,11 +6,13 @@ import eu.eudat.data.entities.Grant;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.rda.Funding;
import javax.transaction.Transactional;
import java.util.Date;
import java.util.UUID;
public class FundingRDAMapper {
@Transactional
public static Funding toRDA(Grant grant) {
Funding rda = new Funding();
String referencePrefix;
@ -22,9 +24,13 @@ public class FundingRDAMapper {
} else {
rda.setFunderId(FunderIdRDAMapper.toRDA(grant.getFunder().getId()));
}
referencePrefix = grant.getReference().split(":")[0];
shortReference = grant.getReference().substring(referencePrefix.length() + 1);
rda.setGrantId(GrantIdRDAMapper.toRDA(shortReference));
if (grant.getReference() != null) {
referencePrefix = grant.getReference().split(":")[0];
shortReference = grant.getReference().substring(referencePrefix.length() + 1);
rda.setGrantId(GrantIdRDAMapper.toRDA(shortReference));
} else {
rda.setGrantId(GrantIdRDAMapper.toRDA(grant.getId().toString()));
}
return rda;
}

33
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/ProjectRDAMapper.java
View File

@ -4,25 +4,34 @@ import eu.eudat.data.entities.Funder;
import eu.eudat.data.entities.Grant;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.rda.Project;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.transaction.Transactional;
import java.util.*;
public class ProjectRDAMapper {
private final static Logger logger = LoggerFactory.getLogger(ProjectRDAMapper.class);
@Transactional
public static Project toRDA(eu.eudat.data.entities.Project project, Grant grant) {
Project rda = new Project();
rda.setTitle(project.getLabel());
rda.setDescription(project.getDescription());
if (project.getStartdate() != null) {
rda.setStart(project.getStartdate().toString());
}
if (project.getEnddate() != null) {
rda.setEnd(project.getEnddate().toString());
}
rda.setFunding(Collections.singletonList(FundingRDAMapper.toRDA(grant)));
if (rda.getTitle() == null) {
throw new IllegalArgumentException("Project Title is missing");
try {
rda.setTitle(project.getLabel());
rda.setDescription(project.getDescription());
if (project.getStartdate() != null) {
rda.setStart(project.getStartdate().toString());
}
if (project.getEnddate() != null) {
rda.setEnd(project.getEnddate().toString());
}
rda.setFunding(Collections.singletonList(FundingRDAMapper.toRDA(grant)));
if (rda.getTitle() == null) {
throw new IllegalArgumentException("Project Title is missing");
}
} catch (Exception e) {
logger.error(e.getLocalizedMessage(), e);
}
return rda;

3
dmp-frontend/src/app/ui/admin/index-managment/index-managment.component.html
View File

@ -1,8 +1,9 @@
<div class="row root">
<mat-card class="col-md-3 offset-md-4">
<div>
<div style="color: red;">Warning: Danger zone. It might delete Dataset tags if not careful</div>
<button mat-raised-button color="primary" (click)="generateIndex($event)" class="lightblue-btn button">Generate Index</button>
<button mat-raised-button color="primary" (click)="clearIndex($event)" class="lightblue-btn button">Clear Index</button>
<!-- <button mat-raised-button color="primary" (click)="clearIndex($event)" class="lightblue-btn button">Clear Index</button> -->
</div>
</mat-card>
</div>

5
dmp-frontend/src/app/ui/auth/login/login.component.ts
View File

@ -54,10 +54,13 @@ export class LoginComponent extends BaseComponent implements OnInit, AfterViewIn
private mergeLoginService: MergeLoginService,
private oauth2DialogService: Oauth2DialogService,
private httpClient: HttpClient,
private matomoService: MatomoService
private matomoService: MatomoService,
) { super(); }
ngOnInit(): void {
if(this.authService.current()){
this.router.navigate(['home']);
}
this.matomoService.trackPageView('loginPage');
this.route.queryParams
.pipe(takeUntil(this._destroyed))

2
dmp-frontend/src/app/ui/dashboard/dashboard.component.html
View File

@ -13,7 +13,7 @@
{{'DASHBOARD.NEW-QUESTION' | translate}} <a href="https://www.openaire.eu/how-to-create-a-data-management-plan" target="_blank"><u>{{'DASHBOARD.OPEN-AIR-GUIDE' | translate}}</u></a> {{'DASHBOARD.LEARN-MORE' | translate}}
</p>
<p *ngIf="this.hasDmps()" class="card-content mb-0 pt-0">{{'DASHBOARD.DMP-ABOUT-BEG' | translate}}
<b>{{'DASHBOARD.DATASET-DESCRIPTIONS' | translate}}</b>
<b>{{'DASHBOARD.DATASET-DESCRIPTIONS-DASHBOARD-TEXT' | translate}}</b>
{{'DASHBOARD.DMP-ABOUT-END' | translate}}
</p>

3
dmp-frontend/src/app/ui/dataset/dataset-wizard/dataset-copy-dialogue/dataset-copy-dialogue.component.ts
View File

@ -61,7 +61,8 @@ export class DatasetCopyDialogueComponent {
const dmpDataTableRequest: DataTableRequest<DmpCriteria> = new DataTableRequest(0, null, { fields: fields });
dmpDataTableRequest.criteria = new DmpCriteria();
dmpDataTableRequest.criteria.like = query;
return this.dmpService.getPaged(dmpDataTableRequest, "profiles").pipe(map(x => x.data), map(x => x.filter(y => this.existsDatasetDescriptionTemplate(y.associatedProfiles))));
dmpDataTableRequest.criteria.datasetTemplates = [this.data.datasetProfileId];
return this.dmpService.getPaged(dmpDataTableRequest, "profiles").pipe(map(x => x.data));
}
existsDatasetDescriptionTemplate(associatedProfiles: DmpAssociatedProfileModel[]): boolean {

2
dmp-frontend/src/app/ui/dataset/overview/dataset-overview.component.ts
View File

@ -173,7 +173,7 @@ export class DatasetOverviewComponent extends BaseComponent implements OnInit {
setIsUserOwner() {
if (this.dataset) {
const principal: Principal = this.authentication.current();
if (principal) this.isUserOwner = principal.id === this.dataset.users.find(x => x.role === Role.Owner).id;
if (principal) this.isUserOwner = !!this.dataset.users.find(x => (x.role === Role.Owner) && (principal.id === x.id));
}
}

4
dmp-frontend/src/app/ui/dmp/editor/add-researcher/add-researcher.component.html
View File

@ -19,8 +19,8 @@
</mat-form-field>
<div class="col-12">
<div class="row">
<div class="ml-auto col-auto"><button mat-raised-button mat-dialog-close type="button">Cancel</button></div>
<div class="col-auto"><button mat-raised-button [disabled]="!isFormValid()" color="primary" (click)="addResearcher()" type="button">Save</button></div>
<div class="ml-auto col-auto"><button mat-raised-button mat-dialog-close type="button">{{'DMP-EDITOR.MAIN-INFO.CANCEL' | translate}}</button></div>
<div class="col-auto"><button mat-raised-button [disabled]="!isFormValid()" color="primary" (click)="addResearcher()" type="button">{{'DMP-EDITOR.MAIN-INFO.SAVE' | translate}}</button></div>
</div>
</div>
</div>

5
dmp-frontend/src/assets/i18n/de.json
View File

@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "Researcher identifier already exists.",
"ORGANISATION-IDENTIFIER-EXSTS": "Organisation identifier already exists.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "This identifier is already used by a researcher in the researchers list.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list.",
"SAVE":"Save",
"CANCEL": "Cancel"
},
"FUNDING-INFO": {
"INTRO": "You are using the DMP editor. Add here information about the scope, funding, actors of your DMP and decide on access and re-use issues for the DMP output that you are creating.",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Personal Usage",
"PUBLIC-USAGE": "Public Usage",
"DATASET-DESCRIPTIONS": "Datasets",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "Datasets",
"PUBLIC-DMPS": "Public DMPs",
"PUBLIC-DATASETS": "Public Datasets",
"RELATED-ORGANISATIONS": "Related Organisations",

5
dmp-frontend/src/assets/i18n/en.json
View File

@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "Researcher identifier already exists.",
"ORGANISATION-IDENTIFIER-EXSTS": "Organisation identifier already exists.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "This identifier is already used by a researcher in the researchers list.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list.",
"SAVE":"Save",
"CANCEL": "Cancel"
},
"FUNDING-INFO": {
"INTRO": "You are using the DMP editor. Add here information about the scope, funding, actors of your DMP and decide on access and re-use issues for the DMP output that you are creating.",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Personal Usage",
"PUBLIC-USAGE": "Public Usage",
"DATASET-DESCRIPTIONS": "Datasets",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "Datasets",
"PUBLIC-DMPS": "Public DMPs",
"PUBLIC-DATASETS": "Public Datasets",
"RELATED-ORGANISATIONS": "Related Organisations",

5
dmp-frontend/src/assets/i18n/es.json
View File

@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "Researcher identifier already exists.",
"ORGANISATION-IDENTIFIER-EXSTS": "Organisation identifier already exists.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "This identifier is already used by a researcher in the researchers list.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list.",
"SAVE":"Save",
"CANCEL": "Cancel"
},
"FUNDING-INFO": {
"INTRO": "You are using the DMP editor. Add here information about the scope, funding, actors of your DMP and decide on access and re-use issues for the DMP output that you are creating.",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Uso personal",
"PUBLIC-USAGE": "Public Usage",
"DATASET-DESCRIPTIONS": "Descripciones de los datasets",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "Descripciones de los datasets",
"PUBLIC-DMPS": "Public DMPs",
"PUBLIC-DATASETS": "Public Dataset Descriptions",
"RELATED-ORGANISATIONS": "Organizaciones relacionadas",

5
dmp-frontend/src/assets/i18n/gr.json
View File

@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "Researcher identifier already exists.",
"ORGANISATION-IDENTIFIER-EXSTS": "Organisation identifier already exists.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "This identifier is already used by a researcher in the researchers list.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list.",
"SAVE":"Αποθήκευση",
"CANCEL": "Ακύρωση"
},
"FUNDING-INFO": {
"INTRO": "You are using the DMP editor. Add here information about the scope, funding, actors of your DMP and decide on access and re-use issues for the DMP output that you are creating.",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Προσωπική Χρήση",
"PUBLIC-USAGE": "Δημόσια Χρήση",
"DATASET-DESCRIPTIONS": "Περιγραφές Συνόλου Δεδομένων",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "Περιγραφές Συνόλου Δεδομένων",
"PUBLIC-DMPS": "Δημόσια Σχέδια Διαχείρισης Δεδομένων",
"PUBLIC-DATASETS": "Δημόσιες Περιγραφές Συνόλου Δεδομένων",
"RELATED-ORGANISATIONS": "Σχετικοί Οργανισμοί",

16
dmp-frontend/src/assets/i18n/pt.json
View File

@ -572,8 +572,8 @@
"PUBLISHED": "Publicado",
"VERSION": "Versão",
"CONTAINED-DATASETS": "Contém Datasets",
"TEXT-INFO": "A informação contida no Plano de Gestão de Dados (PGD) demonstra como os Datasets foram recolhidos e/ou gerados, como foram processados e analisados, que ferramentas, normas e metodologias utilizaram, mas também fornece informação de onde e como os Datasets são alojados, publicados e preservados, incluindo quaisquer custos associados com recursos humanos dedicados a atividades de curadoria/admnistração dos dados ou custos para aquisição ou construção de serviços de gestão de dados.",
"TEXT-INFO-QUESTION": "Não tem a certeza de como um PGD é na prática? Pesquise PGD Públicos e",
"TEXT-INFO": "A informação contida no Plano de Gestão de Dados (PGD) demonstra como os dados foram recolhidos e/ou gerados, como foram processados e analisados, que ferramentas, normas e metodologias utilizaram. Fornece também informação de onde e como os dados são alojados, publicados e preservados.",
"TEXT-INFO-QUESTION": "Não tem a certeza de como um Plano de Gestão de Dados (PGD) é na prática? Pesquise “PGD Públicos” e",
"LINK-ZENODO": "Comunidade LIBER no Zenodo",
"GET-IDEA": "para ter uma ideia!",
"SORT-BY": "Ordenar por",
@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "O identificador do investigador já existe.",
"ORGANISATION-IDENTIFIER-EXSTS": "O identificador da organização já existe.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "Este identificador está já a ser utilizado por um investigador incluído na lista.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "Este identificador está já a ser utilizado por uma organização incluída na lista."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "Este identificador está já a ser utilizado por uma organização incluída na lista.",
"SAVE":"Guardar",
"CANCEL": "Cancelar"
},
"FUNDING-INFO": {
"INTRO": "Um Plano de Gestão de Dados (PGD) permite uma maior proximidade com o local onde os seus dados são gerados, analisados e armazenados. O Argos é uma ferramenta aberta, extensível e colaborativa que disponibiliza Planos de Gestão de Dados FAIR e Abertos.",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Uso Pessoal",
"PUBLIC-USAGE": "Uso Público",
"DATASET-DESCRIPTIONS": "Datasets",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "",
"PUBLIC-DMPS": "PGDs Públicos",
"PUBLIC-DATASETS": "Datasets Públicos",
"RELATED-ORGANISATIONS": "Organizações Relacionadas",
@ -1546,8 +1549,8 @@
"ALL": "TODOS",
"EMPTY-LIST": "Sem Informação",
"LATEST-ACTIVITY": "Última Atividade",
"DMP-ABOUT-BEG": "A criação de um Plano de Gestão de Dados (PGD) no Argos consiste em fornecer informação-chave sobre a investigação, tal como, a sua finalidade, os seus objetivos e quais os investigadores envolvidos, como também sobre a documentação relativa aos dados de investigação",
"DMP-ABOUT-END": "que permite evidenciar os passos dados e os meios utilizados para uma gestão mais eficaz dos dados a produzir ou que já tenham sido produzidos.",
"DMP-ABOUT-BEG": "A criação de um Plano de Gestão de Dados (PGD) no Argos consiste em fornecer informação-chave sobre a investigação, tal como, a sua finalidade, os seus objetivos e quais os investigadores envolvidos, como também sobre a documentação relativa aos dados de investigação que permite evidenciar os passos dados e os meios utilizados para uma gestão mais eficaz dos dados a produzir ou que já tenham sido produzidos.",
"DMP-ABOUT-END": "",
"SELECT-DMP": "Selecione um PGD para o seu Dataset",
"ACTIONS": {
"ADD-DATASET-DESCRIPTION": "Adicione um Dataset",
@ -1793,5 +1796,6 @@
"File format is not supported": "Ficheiro a importar deverá ser em formato .json",
"You cannot Remove Datamanagement Plan with Datasets": "Não pode remover o Plano de Gestão de Dados porque contém pelo menos um modelo de dados associado",
"Failed to create DOI for the Data Management Plan.": "Não foi possível criar um DOI para o Plano de Gestão de Dados",
"No entity found for query": "Não foi possível eliminar o item pretendido"
"No entity found for query": "Não foi possível eliminar o item pretendido",
"Index: 0, Size: 0" : "Ficheiro a importar deverá ser em formato .json"
}

5
dmp-frontend/src/assets/i18n/sk.json
View File

@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "Researcher identifier already exists.",
"ORGANISATION-IDENTIFIER-EXSTS": "Organisation identifier already exists.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "This identifier is already used by a researcher in the researchers list.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list.",
"SAVE":"Save",
"CANCEL": "Cancel"
},
"FUNDING-INFO": {
"INTRO": "Plán manažmentu dát (DMP, z angl. Data Management Plan) tvoria vaše plány manažmentu dát, ktoré sú bližšie miestu, kde sú vygenerované, analyzované a uložené. Argos je otvorený, rozširovateľný, kolaboratívny nástroj, ktorý podporuje plány manažmentu otvorených dát a FAIR dát (Open and FAIR Data Management Plans).",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Osobné použitie",
"PUBLIC-USAGE": "Verejné použitie",
"DATASET-DESCRIPTIONS": "Súbory dát",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "Súbory dát",
"PUBLIC-DMPS": "Verejné DMP",
"PUBLIC-DATASETS": "Verejné súbory dát",
"RELATED-ORGANISATIONS": "Ďalšie organizácie",

5
dmp-frontend/src/assets/i18n/sr.json
View File

@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "Researcher identifier already exists.",
"ORGANISATION-IDENTIFIER-EXSTS": "Organisation identifier already exists.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "This identifier is already used by a researcher in the researchers list.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list.",
"SAVE":"Save",
"CANCEL": "Cancel"
},
"FUNDING-INFO": {
"INTRO": "Plan upravljanja podacima (eng. Data Management Plan) se sastoji od Vaših planova za upravljanje podacima i sadrži informacije kako su nastali, kako su analizirani i na koji način su sačuvani podaci. Argos je otvoren kolaboracioni alat sa mogućnošću nadogradnje i koji podržava otvorene FAIR principe za upravljanje podacima.",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Lična upotreba",
"PUBLIC-USAGE": "Javna upotreba",
"DATASET-DESCRIPTIONS": "Skupovi podataka",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "Skupovi podataka",
"PUBLIC-DMPS": "Javno dostupni Planovi",
"PUBLIC-DATASETS": "Javno dostupni skupovi podataka",
"RELATED-ORGANISATIONS": "Povezane institucije",

5
dmp-frontend/src/assets/i18n/tr.json
View File

@ -1046,7 +1046,9 @@
"RESEARCHER-IDENTIFIER-EXISTS": "Researcher identifier already exists.",
"ORGANISATION-IDENTIFIER-EXSTS": "Organisation identifier already exists.",
"IDENTIFIER-EXISTS-RESEARCHER-LIST": "This identifier is already used by a researcher in the researchers list.",
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list."
"IDENTIFIER-EXISTS-ORGANISATION-LIST": "This identifier is already used by an organisation in the organisations list.",
"SAVE":"Save",
"CANCEL": "Cancel"
},
"FUNDING-INFO": {
"INTRO": "You are using the DMP editor. Add here information about the scope, funding, actors of your DMP and decide on access and re-use issues for the DMP output that you are creating.",
@ -1539,6 +1541,7 @@
"PERSONAL-USAGE": "Kişisel Kullanım",
"PUBLIC-USAGE": "Genel Kullanım",
"DATASET-DESCRIPTIONS": "Veri Setleri",
"DATASET-DESCRIPTIONS-DASHBOARD-TEXT": "Veri Setleri",
"PUBLIC-DMPS": "Herkese açık VYP'ler",
"PUBLIC-DATASETS": "Herkese açık Veri Setleri",
"RELATED-ORGANISATIONS": "Bağlantılı Kurumlar",

2
dmp-frontend/src/assets/splash/index.html
View File

@ -85,7 +85,7 @@
analysed and stored.</p>
</div>
<div class="head-start-dmp">
<a href="/login">
<a href="/home">
<button type="button" class="normal-btn">Start your DMP</button>
</a>
</div>